Realized that these obsolete files are still there.

git-svn-id: http://svn.cactuscode.org/arrangements/CactusPUGHIO/IOStreamedHDF5/trunk@54 0888f3d4-9f52-45d2-93bc-d00801ff5e46

4 files changed, 0 insertions, 1084 deletions

diff --git a/src/DumpVar.c b/src/DumpVar.c
deleted file mode 100644
index 8cb0a2e..0000000
--- a/src/DumpVar.c
+++ /dev/null
@@ -1,365 +0,0 @@
-/*@@
-   @file      DumpVar.c
-   @date      Fri May 21 1999
-   @author    Thomas Radke / Gerd Lanfermann
-   @desc 
-   Do the actual writing of a variable.
-   @enddesc 
-   @history
-   @hauthor Thomas Radke @hdate May 21 1999
-   @hdesc Just copied from thorn FlexIO.
-   @hendhistory
- @@*/
-
-
-#include <stdio.h>
-#include <stdlib.h>
-
-#include "cctk.h"
-#include "cctk_Parameters.h"
-#include "CactusBase/IOUtil/src/ioGH.h"
-#include "CactusPUGH/PUGHSlab/src/PUGHSlab.h"
-#include "StreamedHDF5GH.h"
-
-
-/*#define StreamedHDF5_DEBUG    1 */
-
-/* local function prototypes */
-static void StreamedHDF5_Dump (cGH *GH, int index, int timelevel, void *outme,
-                               int hdim, int *hsizes, int hdf5_type, hid_t fid);
-static void StreamedHDF5_AddCommonAttributes (cGH *GH, int hdim, hid_t dataset);
-static int GetHDF5type (StreamedHDF5GH *myGH, int vtype, hid_t *hdf5_type);
-
-/*@@
-  @routine    StreamedHDF5_DumpVar
-  @date       16 Apr 1999
-  @author     Thomas Radke
-  @desc
-              Generic dump routine, just calls the appropriate dump routine
-	      Extracts the data with Hyperslab.
-  @enddesc
-  @calledby   StreamedHDF5_DumpGH IOHDF5_Write3D
-  @history
-  @endhistory
-  @var        GH
-  @vdesc      Pointer to CCTK grid hierarchy
-  @vtype      cGH
-  @vio        in
-  @endvar
-  @var        index
-  @vdesc      global index of the variable to be dumped
-  @vtype      int
-  @vio        in
-  @endvar
-  @var        timelevel
-  @vdesc      the timelevel to store
-  @vtype      int
-  @vio        in
-  @endvar
-  @var        fid
-  @vdesc      the HDF5 file handle
-  @vtype      hid_t
-  @vio        in
-  @endvar
-@@*/
-int StreamedHDF5_DumpVar (cGH *GH, int index, int timelevel, hid_t fid)
-{
-  DECLARE_CCTK_PARAMETERS
-  void *data;
-  int *hsizes;
-  hid_t hdf5_type;
-  StreamedHDF5GH *myGH;
-  StreamGeo_t geo;
-  int vtype;
-  
-  int sdir[3] = {0,0,0};
-
-
-  /* Get the handle for StreamedHDF5 extensions */
-  myGH = (StreamedHDF5GH *) GH->extensions [CCTK_GHExtensionHandle ("StreamedHDF5")];
-
-  vtype = CCTK_VarTypeI (index);
-  if (GetHDF5type (myGH, vtype, &hdf5_type) < 0)
-  {
-    CCTK_VWarn (1, __LINE__, __FILE__, CCTK_THORNSTRING,
-                "Unsupported variable type %d", vtype);
-    return (-1);
-  }
-  /* shortcut to the slab geometry */
-  geo = myGH->geo_output[index];
-
-  /* get the dimension of the variable */
-
-  hsizes = (int*)malloc(geo.sdim*sizeof(int));
-
-  data = NULL;
-
-  /* TEMPORARY FIX DUE TO INCONSISTENT DIR SPECIFICATION */
-  /* direction vector of 1d line in 3d volume */
-  if (geo.sdim==1) {
-    sdir[0] = (geo.direction[0]==0) ? 1:0;
-    sdir[1] = (geo.direction[0]==1) ? 1:0;
-    sdir[2] = (geo.direction[0]==2) ? 1:0;
-  } 
-  /* norm vector of 2d surface in 3d volume */
-  else if (geo.sdim==2)
-  {
-    sdir[0] = ((geo.direction[0]==1)&&(geo.direction[1]==2)) ? 1:0;
-    sdir[1] = ((geo.direction[0]==0)&&(geo.direction[1]==2)) ? 1:0;
-    sdir[2] = ((geo.direction[0]==0)&&(geo.direction[1]==1)) ? 1:0;
-  }
-  /* spanning directions for 3d */
-  else if (geo.sdim==3)
-  {
-    sdir[0] = geo.direction[0];
-    sdir[1] = geo.direction[1];
-    sdir[2] = geo.direction[2];
-  }
-  else
-    {
-      char *fullname = CCTK_FullName (index);
-      CCTK_VWarn (1, __LINE__, __FILE__, CCTK_THORNSTRING,
-		  "No 0-dim extraction possible: '%s'", fullname);
-      free (fullname);
-      return (-1);
-    }
-
-  if (Hyperslab_GetHyperslab (GH, 0, index, timelevel, geo.sdim, geo.origin,
-                              sdir, geo.length, geo.downs,
-                              &data, hsizes) < 0)
-  {
-    char *fullname = CCTK_FullName (index);
-
-
-    CCTK_VWarn (1, __LINE__, __FILE__, CCTK_THORNSTRING,
-                "Failed to extract hyperslab for variable '%s'", fullname);
-    free (fullname);
-    return (-1);
-  }
-
-  if (fid >= 0)
-  {
-    StreamedHDF5_Dump (GH, index, timelevel, data, geo.sdim, hsizes, hdf5_type, fid);
-  }
-
-  if (data)
-  {
-    free (data);
-  }
-  if (hsizes)
-  {
-    free (hsizes);
-  }
-
-  return (0);
-}
-
-
-/***************************** local functions ****************************/
-
-static int GetHDF5type (StreamedHDF5GH *myGH, int vtype, hid_t *hdf5_type)
-{
-  int retval = 0;
-
-
-  switch (vtype)
-  {
-    case CCTK_VARIABLE_CHAR:
-      *hdf5_type = IOHDF5_CHAR;
-      break;
-    case CCTK_VARIABLE_INT:
-      *hdf5_type = IOHDF5_INT;
-      break;
-    case CCTK_VARIABLE_REAL: 
-      *hdf5_type = IOHDF5_REAL;
-      break;
-    case CCTK_VARIABLE_COMPLEX:
-      *hdf5_type = myGH->IOHDF5_COMPLEX;
-      break;
-    default:
-      retval = -1;
-      break;
-  }
-
-  return (retval);
-}
-
-
-/*@@
-  @routine    StreamedHDF5_AddCommonAttributes
-  @date       May 21 1999
-  @author     Thomas Radke
-  @desc 
-  Add "Common" attributes, these are:
-  <ul>
-    <li> the variable's groupname
-    <li> the grouptype
-    <li> number of timelevels
-    <li> the current date
-         Note that the datestamp should be turned of if you are byte 
-         comparing two output files.
-    <li> simulation time
-    <li> origin
-    <li> bounding box
-    <li> gridspacings (both downsampled and evolution)
-    <li> global grid size
-  </ul>
-  @enddesc 
-  @calledby   StreamedHDF5_DumpGS, IOHDF5_collectiveDump, IOHDF5_procDump
-  @history 
-  @endhistory 
-  @var        GH
-  @vdesc      Pointer to CCTK grid hierarchy
-  @vtype      cGH
-  @vio        in
-  @endvar
-  @var        index
-  @vdesc      global index of the variable to be dumped
-  @vtype      int
-  @vio        in
-  @endvar
-  @var        timelevel
-  @vdesc      the timelevel to store
-  @vtype      int
-  @vio        in
-  @endvar
-  @var        dataset
-  @vdesc      the dataset handle where the attributes should be attached to
-  @vtype      hid_t
-  @vio        in
-  @endvar
-@@*/
-static void StreamedHDF5_AddCommonAttributes (cGH *GH, int hdim, hid_t dataset)
-{
-  DECLARE_CCTK_PARAMETERS
-  CCTK_REAL realAttr [6];
-  StreamedHDF5GH *myGH;
-  CCTK_REAL dummy;
-
-  /* Get the handles for IOUtil and StreamedHDF5 extensions */
-  myGH = (StreamedHDF5GH *) GH->extensions [CCTK_GHExtensionHandle ("StreamedHDF5")];
-
-  WRITE_ATTRIBUTE ("time", &GH->cctk_time, dataset, myGH->scalarDataspace, 0,
-                   IOHDF5_REAL);
-
-  /* NOTE: the attributes "origin", "min_ext", "max_ext", and "delta"
-           are always stored as 3-dimensional points */
-  CCTK_CoordRange (GH, &realAttr [0], &dummy, -1, "x", "cart3d");
-  CCTK_CoordRange (GH, &realAttr [1], &dummy, -1, "y", "cart3d");
-  CCTK_CoordRange (GH, &realAttr [2], &dummy, -1, "z", "cart3d");
-
-  WRITE_ATTRIBUTE ("origin", realAttr, dataset, myGH->arrayDataspace, hdim,
-                   IOHDF5_REAL);
-
-  CCTK_CoordRange (GH, &realAttr [0], &realAttr [3], -1, "x","cart3d");
-  CCTK_CoordRange (GH, &realAttr [1], &realAttr [4], -1, "y","cart3d");
-  CCTK_CoordRange (GH, &realAttr [2], &realAttr [5], -1, "z","cart3d");
-  WRITE_ATTRIBUTE ("min_ext", realAttr, dataset, myGH->arrayDataspace, hdim,
-                   IOHDF5_REAL);
-  WRITE_ATTRIBUTE ("max_ext", realAttr + 3, dataset, myGH->arrayDataspace, hdim,
-                   IOHDF5_REAL);
- 
-  WRITE_ATTRIBUTE ("delta", GH->cctk_delta_space, dataset, myGH->arrayDataspace,
-                   hdim, IOHDF5_REAL);
-}
-
-
-/*@@
-  @routine StreamedHDF5_procDump
-  @author  Thomas Radke
-  @date    May 21 1999
-  @desc    All IO processors dump the data of their group into the file,
-           either as one chunk per processor or unchunked
-           (depending on parameter "unchunked").
-  @enddesc
-  @calledby   StreamedHDF5_DumpGA
-  @history 
-  @endhistory 
-  @var        GH
-  @vdesc      Pointer to CCTK grid hierarchy
-  @vtype      cGH
-  @vio        in
-  @endvar
-  @var        index
-  @vdesc      global index of the variable to be dumped
-  @vtype      int
-  @vio        in
-  @endvar
-  @var        timelevel
-  @vdesc      the timelevel to store
-  @vtype      int
-  @vio        in
-  @endvar
-  @var        outme
-  @vdesc      pointer to the chunk to dump
-  @vtype      void *
-  @vio        in
-  @endvar
-  @var        geom
-  @vdesc      bounds and sizes of the output
-  @vtype      CCTK_INT [3*dim]
-  @vio        in
-  @vcomment   geom [0*dim..1*dim-1]: lower bounds
-              geom [1*dim..2*dim-1]: (local) data sizes
-              geom [2*dim..3*dim-1]: global space
-  @endvar 
-  @var        proc
-  @vdesc      the processor which's chunk is to be dumped
-  @vtype      int
-  @vio        in
-  @endvar
-  @var        hdf5io_type
-  @vdesc      the HDF5 datatype identifier
-  @vtype      int
-  @vio        in
-  @endvar
-  @var        fid
-  @vdesc      the HDF5 file handle
-  @vtype      hid_t
-  @vio        in
-  @endvar
-@@*/
-static void StreamedHDF5_Dump (cGH *GH, int index, int timelevel, void *outme,
-                               int hdim, int *hsizes, int hdf5_type, hid_t fid)
-{
-  DECLARE_CCTK_PARAMETERS
-  int i;
-  hid_t dataset, memspace;
-  char *name, *datasetname;
-  hsize_t *dims;
-
-
-  dims = (hsize_t *)  malloc (hdim * sizeof (hsize_t));
-
-  /* HDF5 needs it in reverse order */
-  for (i = 0; i < hdim; i++)
-  {
-    dims [i] = hsizes [hdim - 1 - i];
-  }
-
-  /* build the unique dataset name */
-  name = CCTK_FullName (index);
-  datasetname = (char *) malloc (strlen (name) + 30);  /* 30 chars should be
-                                                          enough for 2 ints */
-  sprintf (datasetname, "%s@%d@%d", name, GH->cctk_iteration, timelevel);
-  free (name);
-
-  /* create the memspace according to chunk dims */
-  CACTUS_IOHDF5_ERROR (memspace = H5Screate_simple (hdim, dims, NULL));
-
-  /* create the dataset */
-  CACTUS_IOHDF5_ERROR (dataset = H5Dcreate (fid, datasetname, hdf5_type,
-                                            memspace, H5P_DEFAULT));
-  /* write the data */
-  CACTUS_IOHDF5_ERROR (H5Dwrite (dataset, hdf5_type, H5S_ALL, H5S_ALL,
-                                 H5P_DEFAULT, outme));
-
-  StreamedHDF5_AddCommonAttributes (GH, hdim, dataset);
-
-  /* close the dataset and the memspace */
-  CACTUS_IOHDF5_ERROR (H5Dclose (dataset));
-  CACTUS_IOHDF5_ERROR (H5Sclose (memspace));
-
-  free (datasetname);
-  free (dims);
-}
diff --git a/src/ParseGeometry.c b/src/ParseGeometry.c
deleted file mode 100644
index 2241f6c..0000000
--- a/src/ParseGeometry.c
+++ /dev/null
@@ -1,347 +0,0 @@
-
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-
-#include "cctk.h"
-#include "cctk_Arguments.h"
-#include "cctk_Parameters.h"
-#include "cctk_GNU.h"
-#include "util_String.h"
-
-#include "StreamedHDF5GH.h"
-
-/* Do not apply the USE marcro, parser will get confused 
-   by curly braces in quoted strings */
-
-/* CCTK_NO_AUTOUSE_MACRO */
-
-/*$#define HEAVYDEBUG$*/
-
-
-int GeometryParserH5stream(const char *before, char **outname, StreamGeo_t *geo)
-{
-  DECLARE_CCTK_PARAMETERS
-
-  regmatch_t pmatch[3],gmatch[6];
-  int matched, ierr=0,retval=0, verb=0, deb=0;
-
-  const char *argument;
-  char *varname=NULL, *geo_s=NULL;
-  const char *token=NULL; 
-  char *dim_s=NULL, *ori_s=NULL, *dir_s=NULL;
-  char *len_s=NULL, *down_s=NULL;
-
-  int  dim = 0, idim, iidim;
-  int index;
-
-  char info[8000];
-  
-  /* Debugging switches */
-  if (CCTK_Equals(h5verbose,"debug")) {
-    deb  =1;
-    verb =1;
-  }
-  if (CCTK_Equals(h5verbose,"yes"))
-    verb =1;
-      
-  sprintf(info,"\n\nHDF5stream GeometryParser \nargument: >%s<\n",before);
-
-  if((matched = CCTK_RegexMatch(before,
-        	"([A-Za-z][A-Za-z0-9_]*::[A-Za-z][A-Za-z0-9_]*)\\[?(.*)?\\]?", 3, pmatch)) != 0) {
-      if (matched<0) CCTK_WARN(1,"Error matching in GeometryParser");
-#ifdef HEAVYDEBUG
-      printf("matched %d rm_so/rm_eo: %d %d;  %d %d\n",
-             matched,
-             (int)pmatch[1].rm_so,(int)pmatch[1].rm_eo,
-             (int)pmatch[2].rm_so,(int)pmatch[2].rm_eo);
-#endif
-      
-      if(pmatch[1].rm_so != -1 &&
-         (pmatch[1].rm_eo-pmatch[1].rm_so > 0))
-      {
-        varname = (char*) malloc((int)(pmatch[1].rm_eo-pmatch[1].rm_so+1)
-        			 *sizeof(char));
-        strncpy(varname,before+pmatch[1].rm_so,
-        	(int)(pmatch[1].rm_eo-pmatch[1].rm_so));
-        varname[(int)(pmatch[1].rm_eo-pmatch[1].rm_so)]='\0';
-
-        *outname = varname;
-        sprintf(info,"%sOUTNAME : >%s< \n",info,*outname);
-
-        if ((index = CCTK_VarIndex(varname))>=0) {
-          geo->vdim  = CCTK_GroupDimI(CCTK_GroupIndexFromVarI(index));
-        } 
-        else
-        {
-          sprintf(info,"%sOUTNAME : no appropriate gridfunction found:>%s< \n",
-        	  info,*outname);
-          geo->vdim  = -1;
-        }
-      } 
-      else  
-      {
-        CCTK_WARN(1,"No variable name found in StreamedHDF5::out_vars");
-        retval = -1;
-	return(retval);
-      }
-
-      if(pmatch[2].rm_so != -1 &&
-         (pmatch[2].rm_eo-pmatch[2].rm_so > 0))
-      {
-        geo_s = (char*) malloc((int)(pmatch[2].rm_eo-pmatch[2].rm_so+1)
-        		       *sizeof(char));
-        strncpy(geo_s,before+pmatch[2].rm_so,
-        	(int)(pmatch[2].rm_eo-pmatch[2].rm_so));
-        geo_s[(int)(pmatch[2].rm_eo-pmatch[2].rm_so)]='\0';
-        sprintf(info,"%sGEOMETRY: >%s< \n",info,geo_s);
-      } else {
-        sprintf(info,"%sGEOMETRY: No geometry specified -> use default\n",info);
-      }
-  }
-  else {
-    retval=-1;
-    return(retval);
-  }
-
-  /* Pattern match the hyperslab string geo_s*/
-  if (geo_s) {
-    if((matched = CCTK_RegexMatch(geo_s,
-        	  "\\{(.*)\\},\\{(.*)\\},\\{(.*)\\},\\{(.*)\\},\\{(.*)\\}",
-        	  6, gmatch)) != 0) 
-    {
-
-      /* SLAB DIMENSION */
-      if(gmatch[1].rm_so != -1 &&
-         (gmatch[1].rm_eo-gmatch[1].rm_so > 0))
-      {
-        dim_s = (char*) malloc((int)(gmatch[1].rm_eo-gmatch[1].rm_so+1)
-                                 *sizeof(char));
-        strncpy(dim_s,geo_s+gmatch[1].rm_so,
-                (int)(gmatch[1].rm_eo-gmatch[1].rm_so));
-        dim_s[(int)(gmatch[1].rm_eo-gmatch[1].rm_so)]='\0';
-        
-        if (deb)
-          sprintf(info,"%sDIMENSION: >%s< \n",info,dim_s);
-
-        dim = atoi(dim_s);
-        geo->sdim = dim;
-      } 
-      else {
-        if (deb)
-          sprintf(info,"%s","DIMENSION: No dimension\n");
-        retval = -1;
-      }
-      free(dim_s);
-        		  
-      /* DIRECTION */
-      ierr = -1;
-      if(gmatch[2].rm_so != -1 &&
-         (gmatch[2].rm_eo-gmatch[2].rm_so > 0))
-        {
-          dir_s = (char*) malloc((int)(gmatch[2].rm_eo-gmatch[2].rm_so+1)
-                                 *sizeof(char));
-          strncpy(dir_s,geo_s+gmatch[2].rm_so,
-        	  (int)(gmatch[2].rm_eo-gmatch[2].rm_so));
-          dir_s[(int)(gmatch[2].rm_eo-gmatch[2].rm_so)]='\0';
-
-          if (deb)
-            sprintf(info,"%sDIRECTION: >%s< \n",info,dir_s);
-
-          idim = 0;
-          argument = dir_s;
-          while((token = Util_StrSep(&argument,","))) {
-            geo->direction[idim++]=atoi(token);
-          }
-          geo->direction[idim] = atoi(argument);
-          if (idim==dim-1) ierr = 0;
-        }
-      if (ierr<0) {
-        sprintf(info,"%sDIRECTION: dimension not consistent: >%s< (Use default)\n",
-        	info,dir_s);
-      }
-      free(dir_s);
-
-      /* ORIGIN */
-      ierr = -1;
-      if(gmatch[3].rm_so != -1 &&
-         (gmatch[3].rm_eo-gmatch[3].rm_so > 0))
-      {
-        ori_s = (char*) malloc((int)(gmatch[3].rm_eo-gmatch[3].rm_so+1)
-                                 *sizeof(char));
-        strncpy(ori_s,geo_s+gmatch[3].rm_so,
-                (int)(gmatch[3].rm_eo-gmatch[3].rm_so));
-        ori_s[(int)(gmatch[3].rm_eo-gmatch[3].rm_so)]='\0';
-
-        if (deb)
-          sprintf(info,"%sDIRECTION: >%s< \n",info,ori_s);
-
-        idim=0;
-        argument = ori_s;
-        while((token = Util_StrSep(&argument,","))) {
-          geo->origin[idim++]=atoi(token);
-        }
-        geo->origin[idim] = atoi(argument);
-        if (idim==(geo->vdim-1)) ierr = 0;
-        else if (idim==0) {
-          for (iidim=1;iidim<geo->vdim;iidim++)
-            geo->origin[iidim] = geo->origin[0];
-          ierr = 0;
-        }
-      }
-      if (ierr<0) {
-        sprintf(info,"%sORIGIN: dimension not consistent: >%s< \n",
-        	info,ori_s);
-        ierr = -1;
-      }
-      free(ori_s);
-
-      /* LENGTH */
-      ierr = -1;
-      if(gmatch[4].rm_so != -1 &&
-         (gmatch[4].rm_eo-gmatch[4].rm_so > 0))
-      {
-        len_s = (char*) malloc((int)(gmatch[4].rm_eo-gmatch[4].rm_so+1)
-                                 *sizeof(char));
-        strncpy(len_s,geo_s+gmatch[4].rm_so,
-                (int)(gmatch[4].rm_eo-gmatch[4].rm_so));
-        len_s[(int)(gmatch[4].rm_eo-gmatch[4].rm_so)]='\0';
-
-        if (deb)
-          sprintf(info,"%sLENGTH: >%s< \n",info,len_s);
-
-        idim = 0;
-        argument = len_s;
-        while((token = Util_StrSep(&argument,","))) {
-          geo->length[idim++]=atoi(token);
-        }
-        geo->length[idim] = atoi(argument);
-        if (idim==dim-1) ierr = 0;
-        else if (idim==0) {
-          for (iidim=1;iidim<dim;iidim++)
-            geo->length[iidim] = geo->length[0];
-          ierr = 0;
-        }
-      }
-      if (ierr<0) {
-        sprintf(info,"%sLENGTH: dimension not consistent: >%s< (Use Default)\n",
-        	info,len_s);
-      }
-      free(len_s);
-
-      
-      /* DOWNSAMPLING */
-      ierr = -1;
-      if(gmatch[5].rm_so != -1 &&
-         (gmatch[5].rm_eo-gmatch[5].rm_so > 0)) {
-
-        down_s = (char*) malloc((int)(gmatch[5].rm_eo-gmatch[5].rm_so+1)
-                                 *sizeof(char));
-        strncpy(down_s,geo_s+gmatch[5].rm_so,
-                (int)(gmatch[5].rm_eo-gmatch[5].rm_so));
-        down_s[(int)(gmatch[5].rm_eo-gmatch[5].rm_so)]='\0';
-
-        if (deb)
-          sprintf(info,"%sDOWNSAMPLING: >%s< \n",info,down_s);
-
-
-        idim=0;
-        argument = down_s;
-        while((token = Util_StrSep(&argument,","))) {
-          geo->downs[idim++]=atoi(token);
-        }
-        geo->downs[idim] = atoi(argument);
-        if (idim==dim-1) ierr =0;
-        else if (idim==0) {
-          for (iidim=1;iidim<dim;iidim++)
-           geo->downs[iidim] = geo->downs[0];
-          ierr = 0;
-        }
-      }
-      if (ierr<0) {
-        sprintf(info,"%sDOWNSAMPLING: dimension not consistent: >%s< \n",
-        	info,down_s);
-        ierr =-1;
-      }
-      free(down_s);
-    }
-    if (geo_s) free(geo_s);
-  }
-
-  if (verb) {
-    sprintf(info, "%sGeometry Data: \n",info);
-    sprintf(info, "%s  Argument/Slab dimension: %d / %d \n",
-            info,geo->vdim,geo->sdim);
-    sprintf(info, "%s  Origin: ",info);
-    for (idim=0;idim<geo->vdim;idim++)
-      sprintf(info,"%s %d ",info,geo->origin[idim]);
-    sprintf(info,"%s\n  Downs : ",info);
-    for (idim=0;idim<geo->sdim;idim++)
-      sprintf(info,"%s %d ",info,geo->downs[idim]);
-    sprintf(info,"%s\n  Length: ",info);
-    for (idim=0;idim<geo->sdim;idim++)
-      sprintf(info,"%s %d ",info,geo->length[idim]);
-    sprintf(info,"%s\n  Dirs  : ",info);
-    for (idim=0;idim<geo->sdim;idim++)
-      sprintf(info,"%s %d ",info,geo->direction[idim]);
-    sprintf(info,"%s\n\n",info);
-
-    printf("%s",info);
-  }
-
-  USE_CCTK_PARAMETERS
-    
-  return(retval);
-}
-
-void SetDefaultGeoH5stream(StreamGeo_t *geo) {
-  DECLARE_CCTK_PARAMETERS
-
-  int idim;
-  const char *argument, *token;
-
-  geo->vdim = -1;
-  geo->sdim = slabdim;
-
-  /* Origin */
-  idim=0;
-  argument = origin;
-  while((token = Util_StrSep(&argument,","))) {
-    geo->origin[idim++]=atoi(token);
-  }
-  geo->downs[idim] = atoi(argument);
-
-  /* Direction */
-  idim=0;
-  argument = direction;
-  while((token = Util_StrSep(&argument,","))) {
-    geo->direction[idim++]=atoi(token);
-  }
-  geo->downs[idim] = atoi(argument);
-
-  /* Downsample */
-  idim=0;
-  argument = origin;
-  while((token = Util_StrSep(&argument,","))) {
-    geo->downs[idim++]=atoi(token);
-  }
-  geo->downs[idim] = atoi(argument);
-
-  /* Length */
-  idim=0;
-  argument = origin;
-  while((token = Util_StrSep(&argument,","))) {
-    geo->length[idim++]=atoi(token);
-  }
-  geo->length[idim] = atoi(argument);
-
-  for (idim=0;idim<STREAM_MAXDIM;idim++) {
-    geo->direction[idim] = idim;
-    geo->origin[idim]    = 0;
-    geo->length[idim]    =-1;
-    geo->downs[idim]     = 1;
-  }
-
-  USE_CCTK_PARAMETERS
-}
- 
diff --git a/src/ParseVars.c b/src/ParseVars.c
deleted file mode 100644
index 87143ba..0000000
--- a/src/ParseVars.c
+++ /dev/null
@@ -1,208 +0,0 @@
- /*@@
-   @file      GHExtension.c
-   @date      Tue 9th Feb 1999
-   @author    Gabrielle Allen
-   @desc 
-              IOUtil GH extension stuff.
-   @enddesc 
-   @history
-   @endhistory
- @@*/
-
-/*#define DEBUG_IO*/
-
-#include <stdlib.h>
-#include <string.h>
-#include <stdio.h>
-
-#include "cctk.h"
-#include "util_String.h"
-#include "cctk_Parameters.h"
-
-#include "StreamedHDF5GH.h"
-
-
-static char *rcsid = "$Header$";
-
-
-/* =============================================================== 
-   utility routines used by other IO thorns
-   ===============================================================*/
-
- /*@@
-   @routine    IOUtil_ParseVarsForOutput
-   @date       Sat March 6 1999
-   @author     Gabrielle Allen
-   @desc 
-               Sets each flag in the do_output[] do_output to true 
-               if var[i] could be found in the list of variable names.
-               var_list my also contain group names of variables as well as the
-               special keyword "all" which indicates that output is requested
-               on all variables.
-   @enddesc 
-   @history 
-   @endhistory 
-   @var        var_list
-   @vdesc      list of variables and/or group names
-   @vtype      const char *
-   @vio        in
-   @endvar 
-   @var        do_output
-   @vdesc      do_output of flags indicating output was requested for var[i]
-   @vtype      char []
-   @vio        out
-   @endvar 
-@@*/
-
-int ParseVarsForOutputH5stream (StreamedHDF5GH *h5GH, const char *var_list)
-{
-  char *outname=NULL;
-  char *before=NULL;
-  char *after=NULL;
-  char *splitstring;
-  int first,groupnum,i,last,index,varnum;
-  StreamGeo_t geo_tmp;
-  int ierr=0;
-
-  /* First initialise every variable to no output */
-  for (i=0; i<CCTK_NumVars(); i++)
-  {
-    h5GH->do_output[i] = 0;
-  }
-
-  /* Initialize geometry structure with default */
-
-  SetDefaultGeoH5stream(&geo_tmp);
-
-  splitstring = (char *) var_list;
-
-  /* split string at blanks */
-  while(Util_SplitString(&before,&after,splitstring," ")==0) {
-
-#ifdef DEBUG_IO
-    printf("   String is -%s-\n",splitstring);
-    printf("   Split is -%s- and -%s-\n",before,after);
-#endif
-
-    if (CCTK_Equals(before," ")) continue;
-
-    if (strlen(before) > 0) 
-    {
-      /* Extract geometry information */
-      ierr=GeometryParserH5stream(before, &outname, &geo_tmp);
-      if ((ierr<0)||(outname==NULL)) { 
-	CCTK_WARN(1,"GeometryParserH5stream failed.");
-        return(-1);
-      }
-
-      /* Look for any special tokens */
-      if (CCTK_Equals(outname,"all")) 
-      {
-        int ilab;
-        for (ilab=0;ilab<CCTK_NumVars();ilab++) {
-          h5GH->geo_output[ilab]= geo_tmp;
-          h5GH->do_output[ilab] = 1;
-        }
-      } 
-      else 
-      {
-        /* See if this name is implementation::variable */
-        varnum = CCTK_VarIndex(outname);
-        if ( varnum < 0 ) 
-        {
-          /* See if this name is implementation::group */
-          groupnum = CCTK_GroupIndex(outname);
-          if (groupnum < 0) 
-          {
-            char *msg;
-            msg = (char *)malloc((100+strlen(outname))*sizeof(char));
-            sprintf(msg,"Ignoring <%s> in IO string (invalid token)",outname);
-            CCTK_WARN(2,msg);
-            free(msg);
-          } 
-          else 
-          {
-            /* We have a group so now need all the variables in the group */
-            first = CCTK_FirstVarIndexI(groupnum);
-            last = first+CCTK_NumVarsInGroupI(groupnum)-1;
-            for (index=first;index<=last;index++) {
-              h5GH->geo_output[index]=geo_tmp;
-              h5GH->do_output[index] =1;
-            }
-          }
-        } 
-        else
-        {
-          h5GH->geo_output[varnum]= geo_tmp;
-          h5GH->do_output[varnum] = 1;
-        }
-      }
-    }
-    if(before) 
-    {
-      free(before);
-      before = NULL;
-    }
-    if(outname)
-    {
-      free(outname);
-      outname = NULL;
-    }
-    if(splitstring != var_list)
-    {
-      free(splitstring);
-    }
-     
-    splitstring = after;
-
-  }
-
-  if (strlen(splitstring)>0) {
-
-    /* Extract geometry information */
-    ierr=GeometryParserH5stream(splitstring, &outname, &geo_tmp);
-    if (ierr<0) printf("GeometryParser failed: >%s<\n",before);
-
-    /* Special cases */
-    if (CCTK_Equals(outname,"all")) {
-      int ilab;
-      for (ilab=0;ilab<CCTK_NumVars();ilab++) {
-        h5GH->geo_output[ilab]=geo_tmp;
-        h5GH->do_output [ilab]=1;
-      }
-    } else {
-
-      varnum = CCTK_VarIndex(outname);
-      if (varnum < 0) {
-        groupnum = CCTK_GroupIndex(outname);
-        if (groupnum < 0) {
-          char *msg;
-          msg = (char *)malloc((100+strlen(outname))*sizeof(char));
-          sprintf(msg,"Ignoring %s in IO string (invalid token)",outname);
-          CCTK_WARN(2,msg);
-          free(msg);
-        } else {
-          /* We have a group so now need all the variables in the group */
-          first = CCTK_FirstVarIndexI(groupnum);
-          last = first+CCTK_NumVarsInGroupI(groupnum)-1;
-          for (index=first;index<=last;index++) {
-            h5GH->geo_output[index]=geo_tmp;
-            h5GH->do_output[index] =1;
-          }
-        }
-      } 
-      else {
-        h5GH->geo_output[varnum]=geo_tmp;
-        h5GH->do_output[varnum] =1;
-      }
-    }
-  }
-
-  if (before) free(before);
-  if (after) free(after);
-  if(splitstring != var_list)
-  {
-    free(splitstring);
-  }
-  return(0);
-}
diff --git a/src/StreamedHDF5GH.h b/src/StreamedHDF5GH.h
deleted file mode 100644
index 4317db4..0000000
--- a/src/StreamedHDF5GH.h
+++ /dev/null
@@ -1,164 +0,0 @@
- /*@@
-   @header    StreamedHDF5GH.h
-   @date      Fri May 21 1999
-   @author    Thomas Radke
-   @desc 
-   The extensions to the GH structure from StreamedHDF5.
-   @history
-   @hauthor Thomas Radke @hdate May 21 1999
-   @hdesc Just copied from thorn FlexIO.
-   @endhistory
- @@*/
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-
-#include <string.h>
-#include <hdf5.h>
-
-#include "StoreNamedData.h"
-
-
-/* names of the (empty) groups that hold GH extensions or global parameters */
-#define GHEXTENSIONS_GROUP      "GHextensions_group"
-#define GLOBAL_PARAMETERS_GROUP "global_parameters_group"
-#define GLOBAL_PARAMETERS       "global_parameters"
-
-/*****************************************************************************/
-/* some useful macros                                                        */
-/*****************************************************************************/
-/* Check error flags from HDF5 calls */
-#define CACTUS_IOHDF5_ERROR(fn_call)                                          \
-    do {                                                                      \
-      size_t strlen(const char *str);                                         \
-                                                                              \
-      int error_code = fn_call;                                               \
-                                                                              \
-      if (error_code < 0)                                                     \
-        CCTK_VWarn (1, __LINE__, __FILE__, CCTK_THORNSTRING,                  \
-                    "HDF5 call '%s' returned error code %d\n",                \
-                    #fn_call, error_code);                                    \
-    } while (0)
-
-/* macro for writing an attribute */
-#define WRITE_ATTRIBUTE(name, value, dataset, dataspace, dim, datatype)       \
-          do {                                                                \
-            hid_t attr;                                                       \
-            void *val = value;                                                \
-            hsize_t arrayDim = dim;                                           \
-                                                                              \
-            if (H5Tget_class (datatype) == H5T_STRING) {                      \
-              int len = strlen ((char *) val);                                \
-                                                                              \
-              if (len == 0)      /* HDF5 doesn't like zero-len strings */     \
-                len++;                                                        \
-              CACTUS_IOHDF5_ERROR (H5Tset_size (datatype, len));              \
-            }                                                                 \
-            if (arrayDim > 0)                                                 \
-              CACTUS_IOHDF5_ERROR (H5Sset_extent_simple (dataspace, 1,        \
-                                   &arrayDim, NULL));                         \
-            CACTUS_IOHDF5_ERROR (attr = H5Acreate (dataset, name, datatype,   \
-                                 dataspace, H5P_DEFAULT));                    \
-            CACTUS_IOHDF5_ERROR (H5Awrite (attr, datatype, val));             \
-            CACTUS_IOHDF5_ERROR (H5Aclose (attr));                            \
-          } while (0);
-
-/* macro for reading an attribute */
-#define READ_ATTRIBUTE(dataset, attrname, requested_type, buffer)             \
-          { hid_t attr, attrtype;                                             \
-            hsize_t asize = 0;                                                \
-                                                                              \
-            if ((attr = H5Aopen_name (dataset, attrname)) < 0)                \
-              CCTK_WARN (1, "Can't find " attrname " attribute");             \
-            if (requested_type == H5T_C_S1) {                                 \
-              CACTUS_IOHDF5_ERROR (attrtype = H5Aget_type (attr));            \
-              CACTUS_IOHDF5_ERROR (asize = H5Tget_size (attrtype));           \
-              if (asize + 1 >= sizeof (buffer))                               \
-                CCTK_WARN (1, "Can't read " attrname " attribute (too long)");\
-            } else                                                            \
-              attrtype = requested_type;                                      \
-            if (H5Aread (attr, attrtype, buffer) < 0)                         \
-              CCTK_WARN (1, "Can't read " attrname " attribute");             \
-            if (requested_type == H5T_C_S1) {                                 \
-              ((char *) buffer) [asize] = 0;                                  \
-              CACTUS_IOHDF5_ERROR (H5Tclose (attrtype));                      \
-            }                                                                 \
-            CACTUS_IOHDF5_ERROR (H5Aclose (attr));                            \
-          }
-
-
-/* define the HDF5 datatypes according to CCTK_??? datatypes */
-#define IOHDF5_REAL4   H5T_NATIVE_FLOAT
-
-#ifdef  CCTK_REAL_PRECISION_16
-#define IOHDF5_REAL    H5T_NATIVE_LDOUBLE
-#elif   CCTK_REAL_PRECISION_8
-#define IOHDF5_REAL    H5T_NATIVE_DOUBLE
-#elif   CCTK_REAL_PRECISION_4
-#define IOHDF5_REAL    H5T_NATIVE_FLOAT
-#endif
-
-#define IOHDF5_INT     (sizeof (CCTK_INT) == sizeof (int) ?                   \
-                        H5T_NATIVE_INT : H5T_NATIVE_SHORT)
-#define IOHDF5_INT4    (sizeof (int) == 4 ?                                   \
-                        H5T_NATIVE_INT : H5T_NATIVE_SHORT)
-#define IOHDF5_CHAR    H5T_NATIVE_CHAR
-
-#define STREAM_MAXDIM 5
-
-/* Geometry information structure for output variable */
-typedef struct 
-{
-  int vdim;
-  int sdim;
-  int direction[STREAM_MAXDIM];
-  int origin[STREAM_MAXDIM];
-  int length[STREAM_MAXDIM];
-  int downs[STREAM_MAXDIM];
-} StreamGeo_t;
-
-
-/* StreamedHDF5 GH extension structure */
-typedef struct StreamedHDF5GH
-{
-  /* how often to output */
-  int  out_every;
-
-  /* flags indicating output for var [i] */
-  char        *do_output;
-  StreamGeo_t *geo_output;
-
-  /* the last iteration output */
-  int   *out_last;
-
-  /* variables holding the original error printing routine and its argument */
-  H5E_auto_t printErrorFn;
-  void      *printErrorFnArg;
-
-  /* predefined dataspaces for writing scalar and array attributes */
-  hid_t scalarDataspace, arrayDataspace;
-
-  /* predefined datatype for writing CCTK_COMPLEX types */
-  hid_t IOHDF5_COMPLEX;
-
-  /* predefined datatype for writing C string string attributes */
-  hid_t IOHDF5_STRING;
-
-  /* the socket to pass to the Stream VFD */
-  int socket;
-
-} StreamedHDF5GH;
-
-/* function prototypes */
-void StreamedHDF5_Write (cGH *GH, int index, const char *alias);
-void StreamedHDF5_DumpParams (cGH *GH, hid_t group);
-void StreamedHDF5_DumpGHExtensions (cGH *GH, hid_t group);
-int StreamedHDF5_DumpVar (cGH *GH, int index, int timelevel, hid_t iof);
-int ParseVarsForOutputH5stream (StreamedHDF5GH *h5GH, const char *var_list);
-void SetDefaultGeoH5stream(StreamGeo_t *geo);
-int GeometryParserH5stream(const char *before, char **outname, StreamGeo_t *geo);
-
-#ifdef __cplusplus
-} // extern "C" {
-#endif